AS 332 Simply inherited traits Notes PDF

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AS 332 notes on simply inherited traits...

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Simply-inherited traits AS 332 Livestock Breeding & Genetics Simply-Inherited, Polygenic, Qualitative, and Quantitative Traits Polled/horns is an example of a simply-inherited trait, which is a trait affected by only one or a few loci. Assuming you know the genotypes of your animals for a simply-inherited trait, selection and mating decisions are simple, relative to more complex traits. Selecting for polled cattle is relatively straightforward: avoid mating cattle that have horns. Ideally, you would also avoid mating polled cattle that are carrying the “horns” allele. Carriers can be identified by DNA testing. Even without DNA testing, you could reduce the frequency of the “horns” allele to low levels (< 0.10) by simply selecting against horned calves. Of course, genetic selection for most traits is not this simple. Many traits are polygenic traits, which are traits affected by many loci, plus environmental factors. Examples of polygenic traits include weaning weight and meat tenderness in beef cattle, milk and fat yield in dairy cattle, average daily gain and backfat thickness in swine, racing speed in horses, and fleece length in sheep. Unlike simply-inherited traits, a simple “genotype” for polygenic traits does not exist because trait values are influenced by many loci. For polygenic traits, we estimate an animal’s genetic value by calculation of expected progeny differences (EPDs), which we will discuss in a later chapter. Polygenic traits can be further divided into 2 categories: 1) quantitative traits and 2) qualitative traits. Quantitative traits are expressed numerically and include traits where an animal’s phenotype cannot be placed into an obvious, or consistent, category. Examples of quantitative traits include birth weight, weaning weight, average daily gain, Warner-Bratzler Shear Force (meat tenderness), milk yield, protein yield, racing speed, backfat thickness, and fleece length. Qualitative traits are traits where an animal’s phenotype can be placed into obvious categories, such as calving ease (no pull, easy pull, hard pull), twinning (twins, no twins), disease susceptibility (infected, not infected), and fertility (pregnant, open). All simplyinherited traits are also qualitative traits. To review, the 3 categories of traits include 1) Simply-inherited, qualitative, 2) Polygenic, qualitative (also known as a “threshold” trait), and 3) Polygenic, quantitative. Simply-inherited, quantitative traits are extremely rare and for this course, we will ignore this trait category. To differentiate between a qualitative and quantitative trait, you should ask yourself whether the trait value can be placed into discrete categories. If the trait meets this criterion, then the trait is qualitative. For example, cattle can be placed into 2 categories based on presence of horns: 1) horned and 2) polled. Females can also be placed into 2 categories based on fertility: 1) pregnant and 2) open. The qualitative traits can then be further divided into categories based on the number of loci affecting the trait. Only one locus affects polled vs. horns in cattle, so this qualitative trait is simply-inherited. Many loci plus environmental effects affect fertility, so this qualitative trait is polygenic. Quantitative traits cannot be placed into easily defined categories 1 such as milk yield and weaning weight.

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Selecting against genetic abnormalities Most genetic abnormalities are simply-inherited traits; that is, only one locus affects whether an animal expresses a genetic abnormality. For this reason, selection against a genetic abnormality is much simpler than selecting for polygenic traits, which are controlled by many loci. Most (but not all) genetic abnormalities are also caused by a completely recessive allele. Therefore, the recessive allele will not be detected in heterozygous animals except if you use DNA testing, or the abnormality appears in an animal’s offspring. Most genetic abnormalities are also fatal and homozygous recessive animals do not live long enough to contribute progeny to the next generation. If the diseased animals don’t live long enough to produce progeny, then how does a genetic abnormality manage to keep appearing in a herd or breed? The answer is that the recessive alleles are still present in the breed, but are “hiding” in heterozygotes (or carriers). As we discussed in our population genetics lectures, most of the recessive alleles will be found in heterozygotes when the frequency of the recessive allele is low, as is common with most genetic abnormalities. How do you rid your herd of a genetic abnormality, or prevent a genetic abnormality from entering your herd? 1. Avoid purchasing animals that carry genetic abnormalities. A DNA test can be used to test potential sires for genetic abnormalities before purchasing an animal or semen. Some breed associations require DNA testing for certain genetic abnormalities before an animal can be registered with the breed association. Pay close attention to animals that can be traced back to a known carrier or a line that is known to be segregating the genetic abnormality. 2. Use crossbreeding. Most genetic abnormalities can be found in only a few breeds and are completely recessive. Because you need 2 copies of a recessive allele to express a genetic abnormality, you can significantly reduce your risk of finding a abnormality by mating your females to a different, unrelated breed. For example, if you had a herd of Angus cattle and you mated your Angus cows to a Limousin bull, you would significantly reduce your risk of finding a genetic abnormality in the resulting progeny. The Limousin breed has not reported observing many of the genetic abnormalities reported in the Angus breed (AM, NH, and fawn calf syndrome, for example). If half of your genetics is derived from a breed that does not carry a genetic abnormality, then the worst that can happen is the progeny may be carriers of the genetic mutation. For this reason, most mongrel dogs are free from the genetic abnormalities that are found in purebred canines. Many genetic abnormalities in dogs are also completely recessive and require both copies of the recessive allele to express the genetic abnormality. Like most species, canine genetic abnormalities are often only found in a single breed. Mongrels may actually carry many alleles that can cause genetic abnormalities, but because mongrels are a mix of several dog breeds, they rarely carry both recessive alleles. 3. Study the pedigrees of your animals. For some genetic abnormalities (HYPP, for example), the genetic abnormality can be traced back to a popular sire. Scrutinize the pedigrees of your

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animals for links to lines that can be traced back to a known carrier of a genetic abnormality. If you can find a known carrier in an animal’s pedigree, you likely will need to take extra precautions to ensure that your animal does not also carry the genetic abnormality. If, however, the parents (or all 4 grandparents) of an animal has been proven to be noncarriers, you can be sure that this animal does not carry the genetic abnormality. For example, if a foal can be traced back to the stallion Impressive (which spread the HYPP genetic abnormality throughout the Quarter Horse breed), yet the foal’s parents both tested negative for the HYPP allele, you don’t need a DNA test to prove the foal is a non-carrier. If both parents did not carry the HYPP allele, then the HYPP allele cannot be transmitted to the foal, regardless of whether Impressive was in the foal’s bloodline. 4. Consider the use of DNA testing. You don’t need DNA testing for completely dominant genetic abnormalities (Napole in pigs, for example) because you can easily identify carriers and you often don’t need DNA testing for partially dominant genetic abnormalities, either. However, most genetic abnormalities are recessive and in this case, DNA testing can help identify carriers of a genetic abnormality. Depending on cost of the DNA test and the benefit to you as a breeder, you could: a) Test only your sires. b) Test your sires and replacement females. c) Test all of your animals. Sires are often the most important animals to test for a genetic abnormality because often they produce many more progeny than a single female animal. DNA tests have been developed for almost all of the more common genetic abnormalities found in livestock and horses. 5. Don’t breed carriers if progeny will be used as seedstock or kept as replacements. In some instances, you may wish to continue breeding a carrier because a carrier may be genetically very valuable for other traits. Often, you will be able to find a sire equally valuable, but that does not carry the genetic abnormality. Therefore, you may first wish to find a sire of similar genetic value, but that does not carry the mutation. If you must breed a known carrier, you need to be very careful to breed the carrier to only known non-carriers. All progeny from the carrier animal should be tested for the genetic abnormality, and only replacements that do not carry the mutation should be retained. If, however, 1) the progeny will not be used as seedstock or replacements (feeder calves, for example), and 2) the mates are known non-carriers, then you can still safely mate carrier animals. 6. Ethics. You should, under no circumstances, fail to report that an animal carries a genetic abnormality if you know that an animal is a carrier. Failure to report this information is unethical, bad for your breed, and reflects poorly on your business as a breeder. It’s not as easy as it appears to act ethically. You may be under tremendous pressure to earn a profit and a genetic abnormality could hurt your bottom line. Try to remember the long-term consequences of unethical behavior. You may earn a profit in the short-term, but your reputation and the reputation of your breed will be hurt in the end. List of genetic abnormalities in livestock and horses

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This list is not comprehensive. DNA testing for these genetic abnormalities (and confirmation that an animal is a non-carrier) may be necessary before registering an animal with a breed association. Mutations are almost certainly segregating in all breeds of animals, and by no means does this list imply that some breeds are segregating more or less genetic abnormalities. Beef cattle: Arthrogryposis Multiplex (AM) – Formerly called “Curly Calf”. The allele that causes AM is completely recessive to the normal allele. The mutation is found in the Angus breed and may be present in any breed that has been Angus influenced. Calves with AM have stiff joints, the spine is twisted and curved, and less muscle mass is present. These calves usually cause dystocia and often must be delivered by C-section. The abnormality is fatal. AM has been traced back to the bull Rito 9J9. A DNA test is commercially available.

(Picture from http://www.angus.org)

Beef cattle: Neuropathic Hydrocephalus (NH) – Formerly called “severe hydrocephalus”. The NH abnormality is completely recessive to the normal allele. The mutation is found in the Angus-based cattle. Calves with NH are not born alive, have enlarged, deformed craniums, and low birth weights. NH has been traced back to the bull GAR Precision 1680. A DNA test is commercially available. Hydrocephalus can also be found in the Shorthorn and Hereford breeds, although the genetic mutation causing hydrocephalus in these breeds is different than the Angus mutation.

(Picture from the North American Limousin Foundation, courtesy of Dr. David Steffen, U. Nebraska.) Beef cattle: Tibial Hemimelia (TH) – The TH allele is completely recessive to the normal allele. The abnormality is found in Shorthorn, Maine Anjou, and Galloway breeds. The abnormality is characterized by short, deformed limbs (especially the rear limbs), abdominal hernias, and an exposed cranium, spinal cord, or both. The abnormality is lethal. A DNA test is commercially available.

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Dr. Jon Beever, University of Illinois Beef cattle: Pulmonary Hypoplasia with anasarca (PHA) – The PHA allele is completely recessive to the normal allele. The abnormality is found in Maine Anjou and Shorthorn breeds, and the disorder is characterized by poorly formed lungs and retained fluids. The volume of retained fluid can be substantial and even cause dystocia.

Dr. Jon Beever, University of Illinois Beef cattle: Dwarfism – Dwarfism can be caused by several genetic mutations, most of which are completely recessive. However, at least one of the mutations is partially dominant; one copy of the abnormalityive allele causes a compressed body conformation, and 2 copies of the abnormalityive allele causes dwarfism and eventual death. Dwarfism can also be caused by nongenetic factors, so not all dwarfs are caused by genetic abnormalities. Dwarfism was a serious problem for Hereford and Angus breeders in the 1950s. Until recently, the disorder had not been observed in these breeds since the 1970s. Dwarfism has also been observed in Dexter (“bulldog” dwarfs), Brahman, Shorthorn, and Holstein cattle. To my knowledge, commercial DNA tests are unavailable, probably because dwarfism can be caused by abnormalities at many different loci.

Virginia Tech Image Database Beef cattle: Osteopetrosis – Also called “marble bone disease”. The abnormalityive allele is completely recessive to the normal allele. The abnormality is found in Angus and Red Angus cattle. Cattle with this disorder have lower bone densities and, if not born dead, will die shortly after birth. DNA tests are available.

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(Osteopetrosis calf - Picture from the North American Limousin Foundation, courtesy of Dr. David Steffen, U. Nebraska.) Beef cattle: Syndactyly – Also called “mulefoot”. The abnormalityive allele is completely recessive to the normal allele. The abnormality is found in the Angus breed. The abnormality causes webbed toes and is not lethal, although afflicted cattle are not tolerant to heat stress. To my knowledge, a DNA test for syndactyly is not commercially available.

(Schalles, R.R., H.W. Leipold, & R.L. McCraw. Congenital abnormalities in cattle. Beef Cattle Handbook.) Beef cattle: Heterochromia Irides – Also called “white eyes”. The abnormalityive allele is completely recessive to the normal allele. The abnormality is found in black Angus. Coat color of afflicted cattle is brown and from a distance, the eyes appear white. A commercial DNA test is not available. Beef cattle: Hypotrichosis – Also called “hairlessness”. The abnormalityive allele is completely recessive to the normal allele. The abnormality is found in Herefords and results in hairless cattle, although the extent of hairlessness varies by season. A commercially available DNA test is available.

(Picture from the North American Limousin Foundation, courtesy of Dr. Jon Beever, U. Illinois.) Beef cattle: Contractural Arachnodactyly – Formerly called “fawn calf syndrome”. The abnormalityive allele is completely recessive. The abnormality has been observed in Australia for many years before being recognized in the USA. The abnormality is found in the Angus breed and is characterized by stiff joints and reduced range of movement. The abnormality is not fatal and calves who have the disorder can go unnoticed. A DNA test for CA was finally developed and being marketed by Pfizer and Igenity.

(Contractural Arachnodactyly, American Angus Association)

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Beef cattle: Idiopathic epilepsy (IE) – The mutant allele is completely recessive to the normal allele. This genetic abnormality is found in Hereford cattle. The abnormality causes seizures in calves. A DNA test for IE is commercially available. The calves appear normal before the seizures start, so no picture is available. Beef cattle: Protoporphyria – Also called “photosensitivity”. The mutant allele is completely recessive to the normal allele. This genetic abnormality was found in Limousin cattle in the 1970s, and to my knowledge, has been effectively eradicated from the breed. Cattle with this genetic abnormality are sensitive to light, develop open sores when exposed to sunlight, and may suffer from seizures. A DNA test is available, but to my knowledge, the DNA test is not commercially available as this abnormality is currently not a major concern for the Limousin breed.

(Picture from the North American Limousin Foundation, Kent Andersen.) Horses: Hyperkalemic periodic paralysis (HYPP) – The mutant (HYPP) allele is partially dominant to the normal allele. The HYPP allele can be traced back to the Quarter Horse stallion “Impressive”. Horses homozygous for the genetic abnormality experience strong muscle tremors, paralysis, and often die from the disease. Horses carrying only one mutant allele have less severe disease signs and can live productive lives if their diet is controlled by avoiding feedstuffs that are high in potassium. A DNA test is commercially available. Below is a picture of Impressive.

(Spier, S.J. “HYPP: getting to grips with Hyperkalemic Periodic Paralysis.” http://www.horsetalk.co.nz/) Horses: Overo lethal white syndrome (OLWS) – The allele that causes lethality is completely recessive to the normal allele. The lethal allele is found in Paint Horses. Horses born with this genetic abnormality have a part of their intestines missing, which leads to death shortly after birth. The abnormality also results in brain damage. A DNA test for this abnormality is commercially available. OLWS is a very interesting genetic abnormality, as the lethality allele has a “pleiotropic” effect 2 on both health of the horse (whether the horse has an intestinal blockage or not) and white spotting, or overo, coloration. With respect to overo coat coloration, no dominance is

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present at this locus, i.e., one copy of the “lethal” allele results in overo coat color, while 2 copies of the “lethal” allele results in a completely white horse. Unfortunately, horses with 2 copies of the allele also die shortly after birth. Mating 2 overo horses that are carriers of the “lethal” allele will result in a 25% probability of producing a foal with OLWS. To complicate the genetics of OLWS further, not all horses with the overo coloration pattern have a copy of the “lethal” allele. The overo coat coloration pattern can be caused by several different loci, including “modifying loci” which influence the degree of overo patterning in the horse. As a result, mating 2 overo horses will not necessarily result in a 25% chance of producing a foal with OLWS. Additionally, a small percentage of completely white horses do not have OLWS. Overo horses do not always carry the “lethal” allele that causes OLWS. If you breed 2 Paint Horses, it is advisable to test for the presence of the “lethal” allele, especially if one or both horses are overo.

(Horse with OLWS. Notice the horse is completely white. Not all foals that are completely white will have OLWS, but many will. Photo from Animal Genetics, Inc., at http://www.horsetesting.com/) Horses: Glycogen branching enzyme deficiency (GBED) – This genetic abnormality is completely recessive to the normal allele. The genetic abnormality is found in Quarter Horses and Paint Horses. Affected foals cannot store glycogen properly, which eventually results in death. The abnormality may also cause an abortion or stillbirth. The lethal allele may have a frequency as high as 0.10 within the Quarter Horse breed. A DNA test is commercially available. Horses: Severe combined immunodeficiency (SCID) – This genetic abnormality is completely recessive to the normal allele. The genetic abnormality is found in Arabian and Arabian crossbred horses. Foals are born without lymphocytes, a cell type responsible for the generation of an acquired immune response. Therefore, these animals are more prone to becoming infected by pathogens and the severity of infections is often greater, even resulting in death. A DNA test is commercially available. Horses: Hereditary equine regional dermal asthenia (HERDA) – Also known as “Hyperelastosis cutis”. The genetic abnormality is completely recessive to the normal allele. The genetic abnormality is foun...